Causes and consequences of variation in the mammalian microbiota

The mammalian gut teems with a particularly dense and diverse microbial community, the composition of which varies widely among hosts. A large body of laboratory work suggests these communities provide important functions for the host – including nutrition, pathogen protection and immune development – but we know very little about what shapes the mammalian gut microbiota, and how it affects the host, in natural populations. A major barrier to progress is a lack of powerful investigative tools for most wild animal species. I will overcome this by studying a natural population of the species that has the best laboratory tools, and knowledge, for the mammalian microbiome: the house mouse. Specifically, I will set up a new wild house mouse system and use it to address three broad questions: 1) what drives natural variation in the gut microbiota? 2) does microbiota variation predict fitness traits in the wild? and, critically, 3) does microbiota variation causally affect fitness-relevant traits? To do this, I will pair detailed, longitudinal studies of wild mice with controlled experiments in the lab, making use of state-of-the-art tools for this species, including: (i) faecal transplant experiments with germ-free animals, to test the phenotypic impact of different wild mouse microbiotas (ii) high resolution genotyping methods and (iii) new radio-frequency identification (RFID) technology we have recently developed for monitoring wild rodent survival and behaviour.By doing so, this project will directly tackle the key unanswered question: does the composition of the mammalian gut microbiota actually matter in nature?